In the Training scene where the code talkers are doing a transcription from an audio recording, we briefly see the machine playing the audio. The first Wire Recorder was not manufactured by Webster-Chicago until 1948. The machine used in Windtalkers is the "Webcor Model 181 Wire Recorder" which was not manufactured by Webster-Chicago until 1953. The movie is supposed to be set in the early 1940s.
The start of the Camp Pendleton sequence opens with a closeup of a 50-star U.S. flag which is incorrect for 1943, the year of the action. The closeup dissolves to an establishing shot of the camp's parade square where a correct, 48-star flag is visible on the mast. The U.S. would not require a 50-star flag until 1959.
Just before Pete Anderson joins Private Whitehorse in their flute/harmonica-duo, Whitehorse plays solo. However, the flute plays on, just for a second while he is clearly taking in air, and thus, obviously, cannot play.
When the marines first land on Saipan there is a huge battle going on. Nicholas Cage stops to reload his Thompson and has a brief flashback to what happened to him on the Solomon islands. He then finishes reloading and runs up to a Japanese soldier who is on fire. If you look to the right of the screen as he is running, a man in all black is visible wearing goggles - obviously there for fire safety
Throughout the battle of Saipan, no Commissioned Officer is seen. The highest ranking character is the "Gunny" (a generic term for Marines above the rank of Sergeant). A Captain or a Major would be leading such an advance as is shown.